The identification and analysis of chromosome preparations has previously depended on staining methods which produce characteristic chromosome banding patterns unique for every chromosome. The resolution of the method is low, and small rearrangements, including some deletions and duplications, are undetectable. This has led to the introduction of fluorescence in situ hybridization (FISH) techniques using DNA probes which can anneal to complementary sequences on chromosomes and thus act as specific markers. The probes annealed in this way are commonly labeled by haptens and detected indirectly by fluorescent-antibodies, or detected directly by fluorochromes incorporated into the probe itself. The specificity of the probe depends on its DNA sequence and the size of the signal depends on the length of the sequence. Many types of DNA probe are cloned in plasmid, cosmid, yeast artificial chromosome or other vector.
Another class of DNA probe uses total genomic DNA from either complete nuclear DNA or from fractions of nuclear DNA, which can be generated from a variety of sources including whole cells and specific chromosomes. The usual method of preparing these complex probes is by DNA amplification using the polymerase chain reaction (PCR) and random DNA primers. The label is incorporated during the amplification procedure or by nick-translation following amplification. Hybridization of these probes to chromosomes results in a more or less uniform series of fluorescent signals throughout the length of the chromosome. This has been referred to as "chromosome painting" and the probes producing this effect have been termed chromosome paints.
Paints corresponding to individual chromosomes (chromosome-specific paints) can be prepared from PCR amplification of flow sorted chromosomes. They have proved to be useful in the detection and identification of chromosome aberrations beyond the resolution of standard cytogenetic banding methods. Several chromosome specific paints can be used together to detect multiple target chromosomes provided different fluorochromes are used for labeling the probes derived from different chromosomes. For a more detailed description of modem cytogenetic techniques see Ferguson-Smith and Andrews, 1996, "Cytogenetic Analysis," Chapter 12 in Emery & Rimoin's PRINCIPLES & PRACTICE OF MEDICAL GENETICS, edited by D. L. Rimoin et al., Churchill-Livingstone, London. In addition, human chromosome specific paints have been used to identify homologies in non-human species by comparative genome analysis (Wienberg & Stanyon, 1995, Curr. Opin. Gen. & Dev. 5:792-97).